Biomedical Ontology PHI 548 / BMI 508

Biomedical Ontology PHI 548 / BMI 508
Werner Ceusters and Barry Smith

Lecture 8 Representing Types and Representing Instances
Werner Ceusters

Referent Tracking Werner Ceusters
Lecture 8 Part 1 Referent Tracking Werner Ceusters

The focus on (big) data …

Current mainstream thinking
data information knowledge wisdom - representation (- representation)

… makes one forget what data – ideally – are about
Referents References

Current mainstream thinking
data information knowledge wisdom - representation (- representation) References Reality What is there on the side of the patient Questions not often enough asked: What part of our data corresponds with something out there in reality ? What part of reality is not captured by our data, but should because it is relevant ? Referents

A non-trivial relation
Referents References

For instance: source and impact of changes
What are differences in data about the same entities in reality at different points in time due to?

For instance: source and impact of changes
What are differences in data about the same entities in reality at different points in time due to? changes in first-order reality ? changes in our understanding of reality ? inaccurate observations ? differences in perspectives ? registration mistakes ? Ceusters W, Smith B. A Realism-Based Approach to the Evolution of Biomedical Ontologies. AMIA 2006 Proceedings, Washington DC, 2006;:

What makes it non-trivial?
Referents are (meta-) physically the way they are, relate to each other in an objective way, follow ‘laws of nature’. Window on reality restricted by: what is physically and technically observable, fit between what is measured and what we think is measured, fit between established knowledge and ‘laws of nature’. References follow, ideally, the syntactic-semantic conventions of some representation language, are restricted by the expressivity of that language, reference collections need to come, for correct interpretation, with documentation outside the representation. Correspondence with levels of reality? L1: what is real L2: beliefs L3: representations

Generic versus specific entities
Ontology Specific Referent Tracking L3. Representation INFORMATION CONTENT ENTITY ‘WC has migraine’ L2. Beliefs (knowledge) my doctor’s diagnosis DIAGNOSIS L1. First-order reality HUMAN BEING DISEASE LAPTOP MIGRAINE HEADACHE me my headache my migraine my doctor my doctor’s computer

Generic versus specific entities
Ontology Underrepresented majority in information systems! Specific Referent Tracking L3. Representation INFORMATION CONTENT ENTITY ‘WC has migraine’ L2. Beliefs (knowledge) my doctor’s diagnosis DIAGNOSIS L1. First-order reality HUMAN BEING DISEASE LAPTOP MIGRAINE HEADACHE me my headache my migraine my doctor my doctor’s computer

Some early insights The story of Jane Smith an old case, well known in the literature ...
Rector AL, Nowlan WA, Kay S, Goble CA, Howkins TJ. A framework for modelling the electronic medical record. Methods Inf Med Apr;32(2):

July 4th, 1990: Jane goes shopping:
Jane’s favourite supermarket The freezer section of Jane’s favourite supermarket The only available warning sign used outside A very suspiciously shaped upper leg

A visit to the hospital City Health Centre (City HC) Dr. Peters
Dr. Longley

Diagnosis: a severe spiral fracture of the femur

Problem list in an EHR PtID Date ObsCode Narrative 5572 04/07/1990
closed fracture of shaft of femur Fracture, closed, spiral 12/07/1990 Accident in public building (supermarket) 79001 Essential hypertension 0939 24/12/1991 benign polyp of biliary tract 2309 21/03/1992 47804 03/04/1993 Other lesion on other specified region 17/05/1993 298 22/08/1993 Closed fracture of radial head 01/04/1997 PtID Date ObsCode Narrative 20/12/1998 malignant polyp of biliary tract

2 different fracture codes: same (numerically identical) fracture ?
Problem list in an EHR 5572 04/07/1990 closed fracture of shaft of femur Fracture, closed, spiral 12/07/1990 Accident in public building (supermarket) 79001 Essential hypertension 0939 24/12/1991 benign polyp of biliary tract 2309 21/03/1992 47804 03/04/1993 Other lesion on other specified region 17/05/1993 298 22/08/1993 Closed fracture of radial head 01/04/1997 PtID Date ObsCode Narrative 20/12/1998 malignant polyp of biliary tract Same patient, same date, 2 different fracture codes: same (numerically identical) fracture ?

Problem list in an EHR 5572 04/07/1990 closed fracture of shaft of femur Fracture, closed, spiral 12/07/1990 Accident in public building (supermarket) 79001 Essential hypertension 0939 24/12/1991 benign polyp of biliary tract 2309 21/03/1992 47804 03/04/1993 Other lesion on other specified region 17/05/1993 298 22/08/1993 Closed fracture of radial head 01/04/1997 PtID Date ObsCode Narrative 20/12/1998 malignant polyp of biliary tract Same patient, different dates, same fracture codes: same (numerically identical) fracture ?

Problem list in an EHR Different patients, same fracture codes:
5572 04/07/1990 closed fracture of shaft of femur Fracture, closed, spiral 12/07/1990 Accident in public building (supermarket) 79001 Essential hypertension 0939 24/12/1991 benign polyp of biliary tract 2309 21/03/1992 47804 03/04/1993 Other lesion on other specified region 17/05/1993 298 22/08/1993 Closed fracture of radial head 01/04/1997 PtID Date ObsCode Narrative 20/12/1998 malignant polyp of biliary tract Different patients, same fracture codes: Same (numerically identical) fracture ?

Problem list in an EHR Same patient, different dates,
5572 04/07/1990 closed fracture of shaft of femur Fracture, closed, spiral 12/07/1990 Accident in public building (supermarket) 79001 Essential hypertension 0939 24/12/1991 benign polyp of biliary tract 2309 21/03/1992 47804 03/04/1993 Other lesion on other specified region 17/05/1993 298 22/08/1993 Closed fracture of radial head 01/04/1997 PtID Date ObsCode Narrative 20/12/1998 malignant polyp of biliary tract Same patient, different dates, Different codes. Same (numerically identical) polyp ?

Problem list in an EHR Same patient, same hypertension code:
5572 04/07/1990 closed fracture of shaft of femur Fracture, closed, spiral 12/07/1990 Accident in public building (supermarket) 79001 Essential hypertension 0939 24/12/1991 benign polyp of biliary tract 2309 21/03/1992 47804 03/04/1993 Other lesion on other specified region 17/05/1993 298 22/08/1993 Closed fracture of radial head 01/04/1997 PtID Date ObsCode Narrative 20/12/1998 malignant polyp of biliary tract Same patient, same hypertension code: Same (numerically identical) hypertension ?

Problem list in an EHR Different patients. Same supermarket? Maybe the same (irrelevant ?) freezer section ? Or different supermarkets, but always in the freezer sections ? 5572 04/07/1990 closed fracture of shaft of femur Fracture, closed, spiral 12/07/1990 Accident in public building (supermarket) 79001 Essential hypertension 0939 24/12/1991 benign polyp of biliary tract 2309 21/03/1992 47804 03/04/1993 Other lesion on other specified region 17/05/1993 298 22/08/1993 Closed fracture of radial head 01/04/1997 PtID Date ObsCode Narrative 20/12/1998 malignant polyp of biliary tract

CityHC’s representation formalism (for statements in records)
Categories: “represent concepts and are analogous to classes in other formalisms” Individuals: “concrete instances of categories which persist in space and time” Occurrences: “are specific occurrences of individuals and must be situated in space and time. The most important group of occurrences are observations — i.e. agents’ observations of individuals.” Rector AL, Nowlan WA, Kay S, Goble CA, Howkins TJ. A framework for modelling the electronic medical record. Methods Inf Med Apr;32(2):

Main problem areas for CityHC’s EHR:
Statements refer only very implicitly to the concrete entities about which they give information. Idiosyncracies of concept-based terminologies tell us only that some instance of the class the codes refer to, is refered to in the statement, but not what instance precisely. Are usually confused about classes and individuals. “Country” and “Belgium”. Mixing up the act of observation and the thing observed. Mixing up statements and the entities these statements refer to.

Consequences Very difficult to:
Count the number of (numerically) different diseases Bad statistics on incidence, prevalence, ... Bad basis for health cost containment Relate (numerically same or different) causal factors to disorders: Dangerous public places (specific work floors, swimming pools), dogs with rabies, HIV contaminated blood from donors, food from unhygienic source, ... Hampers prevention ...

Ultimate goal of Referent Tracking
A digital copy of the world

In fact … the ultimate crystal ball

Two major representational components
formulae representing ‘laws of nature’ symbols denoting what these ‘laws’ govern

Representations mimicking reality
 The Time Lords’ Matrix on the planet Gallifrey (Dr. Who, )

Major problem: the ‘binding’ wall
How to do it right ? gives you a cartoon of the world

Requirements for this digital copy
R1: A faithful representation of reality R2 … of everything that is digitally registered, what is generic  scientific theories what is specific  what individual entities exist and how they relate ontologically rather than statistically R3: … throughout reality’s entire history, R4 … which is computable in order to … … allow queries over the world’s past and present, … make predictions, … fill in gaps, … identify mistakes, … understand ‘the why’ about realities ...

What is out there … (… we want/need to deal with)?
portions of reality relations configurations ? participation me participating in my life universals entities ? particulars continuants occurrents me my life organism

A faithful representation of reality through BFO
dependent continuant material object spacetime region spatial region temporal region history instanceOf t t t participantOf at t occupies some temporal region some quality my life my 4D STR projectsOn me … at t projectsOn at t some spatial region located-in at t BFO = Basic Formal Ontology

BFO is adequate for R1 … R3 Generic entities Particulars Time indexing

We can do better, can’t we?
Categories: “represent concepts and are analogous to classes in other formalisms” Individuals: “concrete instances of categories which persist in space and time” Occurrences: “are specific occurrences of individuals and must be situated in space and time. The most important group of occurrences are observations — i.e. agents’ observations of individuals.” Rector AL, Nowlan WA, Kay S, Goble CA, Howkins TJ. A framework for modelling the electronic medical record. Methods Inf Med Apr;32(2):

An appropriate ontological analysis
Universals EHR system HC Freezer section Person Femur Fracture Image continuants City HC The freezer section of Jane’s favourite supermarket Jane’s left femur Jane’s left femur fracture Jane Smith Dr. Peters Jane’s fracture’s image Dr. Longley City HC’s EHR system Jane’s falling Jane’s femur breaking Dr. Peter’s examination of Jane’s fracture Dr. Peter’s ordering of an X-ray Shooting the pictures of Jane’s leg occurrents Jane’s fracture’s healing Dr. Peter’s diagnosis making Jane dies Freezer section dismantled Dr. Longley’s examination of Jane’ s fracture t Jane’s fracture as seen by Dr. Peters Jane’s fracture as seen by Dr. Longley Instances of Jane’s fracture

Ontological recategorisation
Fracture Of Femur Severe Spiral Jane Smith’s Fracture Of Femur’s severity shape CityHC Dr. Peters Jane Smith Smith’s Fracture Of Femur Jane Smith’s consultation with Dr. Peters at City HC on 4th July 1990 City HC exists on 4th July 1990 Dr. Peters located at City HC on Dr. Peters’ assessment of Jane Smith’s fracture of femur at City HC on 4th July 1990

Representing specific entities
explicit reference to the individual entities relevant to the accurate description of some portion of reality, ... Ceusters W, Smith B. Strategies for Referent Tracking in Electronic Health Records. J Biomed Inform Jun;39(3):

Method: IUI assignment
Introduce an Instance Unique Identifier (IUI) for each relevant particular (individual) entity 235 78 5678 321 322 666 427 Ceusters W, Smith B. Strategies for Referent Tracking in Electronic Health Records. J Biomed Inform Jun;39(3):

Referent Tracking System Components
Referent Tracking Software Manipulation of statements about facts and beliefs Referent Tracking Datastore: IUI repository A collection of globally unique singular identifiers denoting particulars Referent Tracking Database A collection of facts and beliefs about the particulars denoted in the IUI repository Manzoor S, Ceusters W, Rudnicki R. Implementation of a Referent Tracking System. International Journal of Healthcare Information Systems and Informatics 2007;2(4):41-58.

Key mechanism: IUI assignment
= an act carried out by the first ‘cognitive agent’ feeling the need to acknowledge the existence of a particular it has information about by labelling it with a universally unique singular identifier. ‘cognitive agent’: A person; An organisation; A device or software agent, e.g. Bank note printer, Image analysis software.

Criteria for IUI assignment (1)
The particular’s existence must be determined: Easy for persons in front of you, tools, ... Easy for ‘planned acts’: they do not exist before the plan is executed ! Only the plan exists and possibly the statements made about the future execution of the plan More difficult: a subject’s intensions, emotions But the statements observers make about them do exist ! However: no need to know what the particular exactly is, i.e. which universal it instantiates No need to be able to point to it precisely A member of a specific organization But: this is not a matter of choice, not ‘any’ out of ...

Criteria for IUI assignment (2)
The particular’s existence may not already have been determined ‘as the existence of something else’: Morning star and evening star / Himalaya  2 observers not knowing they observed the same thing May not have already been assigned a IUI. It must be relevant to do so: Personal decision, (scientific) community guideline, ... Possibilities offered by the annotation system If a IUI has been assigned by somebody, everybody else making statements about the particular should use it

Assertion of assignments
IUI assignment is an act of which the execution has to be asserted in the IUI-repository: <da, Ai, td> da IUI of the registering agent Ai the assertion of the assignment <pa, pp, tap> pa IUI of the author of the assertion pp IUI of the particular tap time of the assignment td time of registering Ai in the IUI-repository Neither td or tap give any information about when #pp started to exist ! That might be asserted in statements providing information about #pp .

Referent Tracking assertions
Use these identifiers in expressions using a language that acknowledges the structure of reality: e.g.: a yellow ball: then not : yellow(#1) and ball(#1) rather: #1: the ball #2: #1’s yellow Then still not: ball(#1) and yellow(#2) and hascolor(#1, #2) but rather: instance-of(#1, ball, since t1) instance-of(#2, yellow, since t2) inheres-in(#1, #2, since t2)

The shift envisioned From: To (something like):
‘this man is a 40 year old patient with a stomach tumor’ To (something like): ‘this-1 on which depend this-2 and this-3 has this-4’, where this-1 instanceOf human being … this-2 instanceOf age-of-40-years … this-2 qualityOf this-1 … this-3 instanceOf patient-role … this-3 roleOf this-1 … this-4 instanceOf tumor … this-4 partOf this-5 … this-5 instanceOf stomach … this-5 partOf this-1 … …

‘this man is a 40 year old patient with a stomach tumor’ To (something like): ‘this-1 on which depend this-2 and this-3 has this-4’, where this-1 instanceOf human being … this-2 instanceOf age-of-40-years … this-2 qualityOf this-1 … this-3 instanceOf patient-role … this-3 roleOf this-1 … this-4 instanceOf tumor … this-4 partOf this-5 … this-5 instanceOf stomach … this-5 partOf this-1 … … denotators for particulars

‘this man is a 40 year old patient with a stomach tumor’ To (something like): ‘this-1 on which depend this-2 and this-3 has this-4’, where this-1 instanceOf human being … this-2 instanceOf age-of-40-years … this-2 qualityOf this-1 … this-3 instanceOf patient-role … this-3 roleOf this-1 … this-4 instanceOf tumor … this-4 partOf this-5 … this-5 instanceOf stomach … this-5 partOf this-1 … … denotators for appropriate relations

‘this man is a 40 year old patient with a stomach tumor’ To (something like): ‘this-1 on which depend this-2 and this-3 has this-4’, where this-1 instanceOf human being … this-2 instanceOf age-of-40-years … this-2 qualityOf this-1 … this-3 instanceOf patient-role … this-3 roleOf this-1 … this-4 instanceOf tumor … this-4 partOf this-5 … this-5 instanceOf stomach … this-5 partOf this-1 … … denotators for universals or particulars

‘this man is a 40 year old patient with a stomach tumor’ To (something like): ‘this-1 on which depend this-2 and this-3 has this-4’, where this-1 instanceOf human being … this-2 instanceOf age-of-40-years … this-2 qualityOf this-1 … this-3 instanceOf patient-role … this-3 roleOf this-1 … this-4 instanceOf tumor … this-4 partOf this-5 … this-5 instanceOf stomach … this-5 partOf this-1 … … time stamp in case of referenced continuants

Representation of relation with time intervals

Representation in the EHR
Relevant particulars referred to using IUIs Relationships that obtain between particulars at time t expressed using relations from OBO-Foundry ontology Statements describing for each particular, at time t: Of what universal from an ontology it is an instance of AND/OR (if one insists): By means of what concept from a concept-based system it can sensibly be described particulars CityHC Dr. Peters Jane Smith Smith’s Fracture Of Femur Severe Spiral Jane Smith’s consultation with Dr. Peters at City HC on 4th July 1990 Dr. Peters’ assessment of fracture of femur at Of Femur’s severity shape 4th July 1990

Elementary Referent Tracking tuple types
Relationships between particulars taken from a realism-based relation ontology Instantiation of a universal Annotation using terms from a non-realist terminology ‘Negative findings’ such as absences, missing parts, preventions, … Names for a particular

Dealing with mistakes RTS entries are assigned IUIs of their own which in the restructured D-template is symbolized by IUIti. Di = <IUId, IUIti, t, E, C, S>. IUId: the IUI of the entity annotating IUIti by means of the Di entry, E: either the symbol ‘I’ (for insertion) or any of the error type symbols, C: a symbol for the applicable reason for change t: the time the tuple denoted by IUIti is inserted or ‘retired’, S: a list of IUIs denoting the tuples, if any, that replace the retired one.

Ontology and Referent Tracking: division of labor
instance-of at t #105 caused by

Referent Tracking: An application in adverse event representation

Ontology for Risks Against Patient Safety
Ceusters W, Capolupo M, De Moor G, Devlies J, Smith B. An Evolutionary Approach to Realism-Based Adverse Event Representations. Methods of Information in Medicine, 2011;50(1):62-73.

Representing particular adverse event cases
Is the generic representation of the portion of reality adequate enough for the description of particular cases? Example: a patient born at time t0 undergoing anti-inflammatory treatment and physiotherapy since t2 for an arthrosis present since t1 develops a stomach ulcer at t3. 60 60

Anti-inflammatory treatment with ulcer development
IUI Description of particular Properties #1 the patient who is treated #1 member_of C1 since t2 #2 #1’s treatment #2 instance_of C #2 has_participant #1 since t2 #2 has_agent #3 since t2 #3 the physician responsible for #2 #3 member_of C4 since t2 #4 #1’s arthrosis #4 member_of C5 since t1 #5 #1’s anti-inflammatory treatment #5 part_of # #5 member_of C2 since t3 #6 #1’s physiotherapy #6 part_of #2 #7 #1’s stomach #7 member_of C6 since t2 #8 #7’s structure integrity #8 instance_of C8 since t #8 inheres_in #7 since t0 #9 #1’s stomach ulcer #9 part_of #7 since t3 #10 coming into existence of #9 #10 has_participant #9 at t3 #11 change brought about by #9 #11 has_agent #9 since t #11 has_participant #8 since t3 #11 instance_of C10 (harm) at t3 #12 noticing the presence of #9 #12 has_participant #9 at t3+x #12 has_agent #3 at t3+x #13 cognitive representation in #3 about #9 #13 is_about #9 since t3+x 61 61

Time line and dependencies (1)
the patient (#1) who is treated #1 #1’s stomach #7 #7’s structure integrity #8 structure integrity C8 At t0, the patient is born, and since that time, his stomach is part of him and a structure integrity (C8) inheres in it: #1 instance-of person since t0 #7 part-of #1 since t0 #8 instance_of C8 since t0 #8 inheres_in #7 since t0 62 62

the patient who is treated #1 #1’s stomach #7 #7’s structure integrity #8 structure integrity C8 #1’s arthrosis #4 underlying disease C5 At t1, the patient acquires arthrosis: #4 member_of C5 since t1 #4 inheres_in #1 since t1 63 63

the patient who is treated #1 subject of care C1 #1’s stomach #7 involved structure C6 #7’s structure integrity #8 structure integrity C8 #1’s arthrosis #4 underlying disease C5 #1’s treatment #2 act of care C3 #1’s physiotherapy #6 #1’s anti-inflammatory treatment #5 At t2, the patient consults #3 who starts treatment. It is then that the patient becomes a member of the class subject of care (C1) and his stomach a member of the class involved structure (C6) the physician responsible for #2 #3 care giver C4 64 64

Time line and dependencies …
the patient who is treated #1 subject of care C1 #1’s stomach #7 involved structure C6 #7’s structure integrity #8 structure integrity C8 #1’s arthrosis #4 underlying disease C5 #1’s treatment #2 act of care C3 #1’s physiotherapy #6 #1’s anti-inflammatory treatment #5 act under scrutiny C2 #1’s stomach ulcer #9 change brought about by #9 #11 harm C10 noticing #9 #12 cognitive representation in #3 about #9 #13 the physician responsible for #2 #3 care giver C4 65 65

Referent Tracking: An application in dataset disambiguation

A colleague shares his research data set

A closer look What are you going to ask him right away?
What do these various values stand for and how do they relate to each other? Might this mean that patient #5057 had only once sex at the age of 39?

Step 1: ‘meaning’ of values in data collections
‘The patient with patient identifier ‘PtID4’ is stated to have had a panoramic X-ray of the mouth which is interpreted to show subcortical sclerosis of that patient’s condylar head of the right temporomandibular joint’ 1 meaning

Step 2 (1): list the entities denoted
1(The patient) with 2(patient identifier ‘PtID4’) 3(is stated) 4(to have had) a 5(panoramic X-ray) of 6(the mouth) which 7(is interpreted) to 8(show) 9(subcortical sclerosis of 10(that patient’s condylar head of the 11(right temporomandibular joint)))’ CLASS INSTANCE IDENTIFIER person IUI-1 patient identifier IUI-2 assertion IUI-3 technically investigating IUI-4 panoramic X-ray IUI-5 mouth IUI-6 interpreting IUI-7 seeing IUI-8 diagnosis IUI-9 condylar head of right TMJ IUI-10 right TMJ IUI-11 notes: colors have no meaning here, just provide easy reference, this first list can be different, any such differences being resolved in step 3

Step 2 (2): provide directly referential descriptions
CLASS INSTANCE IDENTIFIER DIRECTLY REFERENTIAL DESCRIPTIONS person IUI-1 the person to whom IUI-2 is assigned patient identifier IUI-2 the patient identifier of IUI-1 assertion IUI-3 'the patient with patient identifier PtID4 has had a panoramic X-ray of the mouth which is interpreted to show subcortical sclerosis of that patient’s right temporomandibular joint' technically investigating IUI-4 the technically investigating of IUI-6 panoramic X-ray IUI-5 the panoramic X-ray that resulted from IUI-4 mouth IUI-6 the mouth of IUI-1 interpreting IUI-7 the interpreting of the signs exhibited by IUI-5 seeing IUI-8 the seeing of IUI-5 which led to IUI-7 diagnosis IUI-9 the diagnosis expressed by means of IUI-3 condylar head of right TMJ IUI-10 the condylar head of the right TMJ of IUI-1 right TMJ IUI-11 the right TMJ of IUI-1

Step 3: identify further entities that ontologically must exist for each entity under scrutiny to exist. assigner role IUI-12 the assigner role played by the entity while it performed IUI-21 assigning IUI-21 the assigning of IUI-2 to IUI-1 by the entity with role IUI-12 asserting IUI-20 the asserting of IUI-3 by the entity with asserter role IUI-13 asserter role IUI-13 the asserter role played by the entity while it performed IUI-20 investigator role IUI-14 the investigator role played by the entity while it performed IUI-4 panoramic X-ray machine IUI-15 the panoramic X-ray machine used for performing IUI-4 image bearer IUI-16 the image bearer in which IUI-5 is concretized and that participated in IUI-8 interpreter role IUI-17 the interpreter role played by the entity while it performed IUI-7 perceptor role IUI-18 the perceptor role played by the entity while it performed IUI-8 diagnostic criteria IUI-19 the diagnostic criteria used by the entity that performed IUI-7 to come to IUI-9 study subject role IUI-22 the study subject role which inheres in IUI-1

Step 3: some remarks interpreter role, perceptor role, …
reference to roles rather than the entity in which the roles inhere because it may be the same entity and one should not assign several IUIs to the same entity each description follows similar principles as Aristotelian definitions but is about particulars rather than universals

Step 4: classify all entities in terms of realism-based ontologies
requires more ontological and philosophical skills than domain expertise or expertise with Protégé, not just term matching CLASS HIGHER CLASS person BFO: Object patient identifier IAO: Information Content Entity assertion technically investigating OBI: Assay panoramic X-ray IAO: Image mouth FMA: Mouth interpreting MFO: Assessing seeing BFO: Process diagnosis IAO: Information Content Entity condylar head of right TMJ FMA: Right condylar process of mandible right TMJ FMA: Right temporomandibular joint assigner role BFO: Role assigning study subject role OBI: Study subject role

Step 5: specify relationships between these entities
For instance: at least during the taking of the X-ray the study subject role inheres in the patient being investigated: IUI-23 inheres-in IUI-1 during t1 the patient participates at that time in the investigation IUI-4 has-participant IUI-1 during t1 These relations need to follow the principles of the Relation Ontology. Smith B, Ceusters W, Klagges B, Koehler J, Kumar A, Lomax J, Mungall C, Neuhaus F, Rector A, Rosse C. Relations in biomedical ontologies, Genome Biology 2005, 6:R46.

Step 6: outline all possible configurations of such entities for the sentence to be true (a one semester course on its own) Such outlines are collections of relational expressions of the sort just described, Variant configurations for the example: perceptor and interpreter are the same or distinct human beings, the X-ray machine is unreliable and produced artifacts which the interpreter thought to be signs motivating his diagnosis, while the patient has indeed the disorder specified by the diagnosis (the clinician was lucky) …

Methodology (2): for each dataset
Build a formal template which describes: the results of steps 4-6 of the 1st order analysis, the relationships between: the 1st order entities and the corresponding data items in the data set, data items themselves. Build a prototype able to generate on the basis of the template for each subject (patient) in the dataset an RT-compatible representation of his 1st and 2nd order entities.

The template

Partial Template for 3 variables (in the ‘German’ dataset)
RN Var RT REF Min Max Val 1 IM patient_study_record 2 id LV patient_identifier 3 patient 4 sex CV gender 5 male 6 female 7 UA BLANK 8 q3 no_pain_in_ lower_face 9 pain_in_ lower_face 10 in_the_past_month 11 lower_face 12 time_of_q3_concretization 13 RP an_8_gcps_1 14 UP 15 16 JA

3 variables in the ‘German’ dataset
RN Var RT REF Min Max Val 1 IM patient_study_record 2 id LV patient_identifier 3 patient 4 sex CV gender 5 male 6 female 7 UA BLANK 8 q3 no_pain_in_ lower_face 9 pain_in_ lower_face 10 in_the_past_month 11 lower_face 12 time_of_q3_concretization 13 RP an_8_gcps_1 14 UP 15 16 JA Answer to the question: ‘Have you had pain in the face, jaw, temple, in front of the ear or in the ear in the past month?’ Answer to the question: ‘’ How would you rate your facial pain on a 0 to 10 scale at the present time, that is right now, where 0 is "no pain" and 10 is "pain as bad as could be"?

Record Types in the template
RN Var RT REF Min Max Val 1 IM patient_study_record 2 id LV patient_identifier 3 patient 4 sex CV gender 5 male 6 female 7 UA BLANK 8 q3 no_pain_in_ lower_face 9 pain_in_ lower_face 10 in_the_past_month 11 lower_face 12 time_of_q3_concretization 13 RP an_8_gcps_1 14 UP 15 16 JA LV: Literal value CV: Coded Value IM: Implicit JA: Justified Absence UA: Unjustified Absence UP: Unjustified Presence RP: Redundant Presence

Condition-based xA/xP determination
RN Var RT REF Min Max Val 7 sex UA BLANK 13 q3 RP an_8_gcps_1 14 UP 1 10 15 16 JA If the value of REF is either outside the range of Min/Max or ‘BLANK’ and the value for Var is as indicated by Val, including no value at all, then the presence or absence of the corresponding data item is of a sort indicated by RT.

Conditional selection of descriptions

RT compatible part of the template
RN IUI(L) IUI(P) P-Type P-Rel P-Targ Trel Time 1 #psrec- dataset-record at t 2 #pidL- #pid- denotator denotes #pat- 3 #patL- patient 4 #patgL- #patg- gender inheres-in 5 male-gender 6 female-gender 7 underspec-ice 8 #q3L0- lacks-pcp pain #tq3- 9 #q3L1- #pq3- participant 10 month-period 11 #patlf- lower-face part-of 12 #cq3- time-period after 13 #q3L- corresp-w 14 disinformation 15 16 j-blank-ice

RN IUI(L) IUI(P) P-Type P-Rel P-Targ Trel Time 1 #psrec- dataset-record at t 2 #pidL- #pid- denotator denotes #pat- 3 #patL- patient 4 #patgL- #patg- gender inheres-in 5 male-gender 6 female-gender 7 underspec-ice 8 #q3L0- lacks-pcp pain #tq3- 9 #q3L1- #pq3- participant 10 month-period 11 #patlf- lower-face part-of 12 #cq3- time-period after 13 #q3L- corresp-w 14 disinformation 15 16 j-blank-ice denotes (when instantiated) the gender of the patient denotes (when instantiated) the data item concretized in the dataset in relation to the gender of the patient

RN IUI(L) IUI(P) P-Type P-Rel P-Targ Trel Time 1 #psrec- dataset-record at t 2 #pidL- #pid- denotator denotes #pat- 3 #patL- patient 4 #patgL- #patg- gender inheres-in 5 male-gender 6 female-gender 7 underspec-ice 8 #q3L0- lacks-pcp pain #tq3- 9 #q3L1- #pq3- participant 10 month-period 11 #patlf- lower-face part-of 12 #cq3- time-period after 13 #q3L- corresp-w 14 disinformation 15 16 j-blank-ice

Work in progress: IAO (?) related types
UNDERSPECIFIED-ICE ICE which describes a portion of reality at determinable rather than determinate level DISINFORMATION GDC which provides erroneous information J-BLANK-ICE GDC which conveys there should not be an ICE concretized.

Biomedical Ontology PHI 548 / BMI 508

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Biomedical Ontology PHI 548 / BMI 508

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Presentation on theme: "Biomedical Ontology PHI 548 / BMI 508"— Presentation transcript:

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About project

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